According to "Affliction"/"Divergence" one Klingon colony world was infected with the Augment virus. Therefore both smooth and bumpy Klingons should have co-existed in the Empire, even though we never saw it on TV or film (this was, however, depicted in the post-series Enterprise novels and a few old TOS ones too)

In Into Darkness we'll see about a dozen Klingons, but only 3 or 4 of them unmasked - and since what's under the masks of the others isn't revealed, some could very well be smooth-headed. So no continuity error, IMO.

That's a good, plausible explanation. Still, I would like to see some smoothed-headed Klingons. It would be a nice homage to TOS. Do we know for certain that there won't be any smoothed-headed Klingons?

Yeah, it was confirmed that all the Klingons whose faces we see have ridges. Prior to filming, writer Bob Orci said simply on Trekmovie.com that "the Klingons have ridges". Much more recently, details have emerged about the nuKlingons faces - see HERE for details.
(it seems I was mistaken about the number of unmasked Klingons seen)